molbox 0.1.4

Create simulation boxes for LAMMPS.

molbox

Molbox is a simple Python package that extends rdkit with spatial transformations of 3D molecules and semantics for multiple molecules in a rectangular box. It allows you to quickly create simulation boxes and write them to data files that can be read by LAMMPS.

Installation

pip install molbox

Usage

from molbox import Box, MolBox
from molbox.lammps_data import write_lammps_data
from molbox.rdkit_3d_ops import create_3d_mol_from_smiles, rotate_mol
from rdkit import Chem
from scipy.spatial.transform import Rotation


def main():
    box = Box([0, 0, 0], [175, 175, 175])
    o2_box = MolBox(box=box)
    o2_mol = create_3d_mol_from_smiles("O=O")
    num_mols = 128
    for _ in range(num_mols):
        rotation = Rotation.random()
        new_mol = rotate_mol(o2_mol, rotation, "COM")
        o2_box.add_mol_randomly(new_mol)
    Chem.MolToMolFile(o2_box.mol, "examples/o2_box.mol")
    write_lammps_data(o2_box, "examples/o2_box.lmpdat")


if __name__ == "__main__":
    main()